How do we build realistic cellular environments for simulations? @cg-martini.bsky.social, @ma3ke.bsky.social, @janstevens.bsky.social answer this with Bentopy, an integration tool for proteomics, metabolomics, and structural data that rapidly assembles simulation-ready molecular models.

Building realistic models of cells means fitting proteins, RNA, and metabolites at experimental concentrations inside complex cellular architectures. Here's a movie showing how we pack the cytoplasmic space of the JCVI-Syn3A cell:

Our paper on [Bentopy](doi.org/10.1002/pro....) is out in Protein Science! We developed Bentopy to make assembling large-scale MD models more accessible, building on what we learned from trying to simulate whole-cell models. Here's our updated Martini JCVI-syn3A cell model👇

So pleased this is finally out! Wonderful work by the incredibly talented @ma3ke.bsky.social and @janstevens.bsky.social to generate densely packed systems, even with complex topologies Go to the paper for cool science, stay for the mesmerizing figures 🤩 Read more about it in this thread 👇

It was great to be a small part of this work with the incredibly talented PhD student Andrea!! If you want to find out how you can save heaps of time while still maintaining accurate results with CG metadynamics, look no further!! Read the article here 👇

My little outlook on how our lungs 🫁 are like the sea 🌊 is finally out in Central Science. Thanks to the support from incredible mentors @rommieamaro.bsky.social and @kprather.bsky.social !!

Kat Blow has developed CCD2MD, a suite of packages for preparing co-folded outputs for MD simulations. Created for protein–lipid interactions in integral membrane proteins, it also works for peripheral and lipid-anchored proteins too. pubs.acs.org/doi/full/10.... github.com/keb721/ccd2md

Martini on top of the world ! TS2CG as a Membrane Builder | Journal of Chemical Theory and Computation pubs.acs.org/doi/10.1021/...

A true community effort ! The Martini 3 Lipidome: Expanded and Refined Parameters Improve Lipid Phase Behavior | ACS Central Science pubs.acs.org/doi/10.1021/...

@chelseabrown.bsky.social @cg-martini.bsky.social@rug.nl Integrative molecular modelling of a mitochondrial crista demonstrates a pipeline for constructing biologically representative systems and addressing interactions in complex environments www.nature.com/articles/s42...

It was great to help out the lipids with these two Mycobacterial enzymes. Fantastic work from the Mancia lab!

What better way to use my first proper post than to share my first big piece of post-doctoral work with @cg-martini.bsky.social! Here, we used integrative modelling to build and simulate a mitochondrial cristae. Find the paper here (rdcu.be/eujAC) or see below for a quick overview 👇

Martini workshop registration now open !!!! See cgmartini.nl for details and how to apply. Looking forward to seeing you in Groningen, Aug 11-15th.

Pre-announcement: MARTINI tutorial workshop, August 11-15th 2025 in Groningen, The Netherlands !! Learn basic and advanced Martini from the cocktail masters themselves. Registration will open soon.

MartiniGlass: a Tool for Enabling Visualization of Coarse-Grained Martini Topologies | Journal of Chemical Information and Modeling pubs.acs.org/doi/10.1021/...